Research workbench
SARS-cov-2 replication-transcription complex bound to NSP13 helicase - NSP13(2)-rtc - swiveled class
Analyse SARS-cov-2 replication-transcription complex bound to NSP13 helicase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RE0
- Type
- protein + RNA
- Length
- 2,624 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7…
- EC
- 2.7.7.48, 3.6.4.12, 3.6.4.13
- UniProt
- P0DTD1
- Ligands
- ADP, AF3, ZN, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 7 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 43% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 186 | 59% helix, 16% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 75 | 76% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 185 | 59% helix, 17% strand | P0DTD1 |
| E, F | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 590 | 25% helix, 18% strand | P0DTD1 |
| P | Product RNA | rna | 34 | — | — |
| T | Template RNA | rna | 37 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, E, F
- AF3 · Aluminum fluoride · ligand · 2 copies · chains E, F
- ZN · Zinc ion · metal · 8 copies · chains A, E, F
- MG · Magnesium ion · metal · 3 copies · chains A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.79 | 0.81 | 85 | empty |
| 2 | 867 | 0.79 | 0.81 | 73 | empty |
| 3 | 127 | 0.77 | 0.96 | 23 | empty |
| 4 | 926 | 0.77 | 0.80 | 108 | ADP, MG, AF3 |
| 5 | 885 | 0.76 | 0.79 | 72 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2507 Ų buried · 12 hydrogen bonds · protein-protein
- P–T · 1572 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- C–D · 1534 Ų buried · 4 hydrogen bonds · protein-protein
- A–T · 1113 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 846 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RE0 · SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7RE0 · PDBe 7RE0 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.